double v(double m, double phi, double v_0, double mu, double k, double l_0)
{
/* Calculates the velocity at a point given the velocity d_phi away
from the point we care about. Derivation explained in lab report.
*/
return sqrt(((2*r*d_phi)/m)*(wt(m,phi)-Fst(phi,k,l_0)-mu*wn(m,phi)
-mu*Fsn(phi,k,l_0)+((mu*m*pow(v_0,2))/(r))
+(m*pow(v_0,2)/(2*r*d_phi))));
}
bool UnitTests::SharedSeqs()
{
std::vector< std::vector<double> > dissMatrix;
// unweighted MRCA (= MRCA restricted Soergel)
DiversityCalculator uMRCA("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Soergel", 1000, false, false, true, false, false);
uMRCA.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 8.0/13.0))
return false;
if(!Compare(dissMatrix[2][0], 8.0/13.0))
return false;
if(!Compare(dissMatrix[2][1], 2.0/6.0))
return false;
// unweighted Tamas coefficient
DiversityCalculator uTC("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Tamas coefficient", 1000, false, false, false, false, false);
uTC.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 8.0/13.0))
return false;
if(!Compare(dissMatrix[2][0], 8.0/13.0))
return false;
if(!Compare(dissMatrix[2][1], 2.0/13.0))
return false;
// unweighted Soergel
DiversityCalculator uSoergel("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Soergel", 1000, false, false, false, false, false);
uSoergel.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 8.0/13.0))
return false;
if(!Compare(dissMatrix[2][0], 8.0/13.0))
return false;
if(!Compare(dissMatrix[2][1], 2.0/9.0))
return false;
// unweighted Canberra
DiversityCalculator uCanberra("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Canberra", 1000, false, false, false, false, false);
uCanberra.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 8.0))
return false;
if(!Compare(dissMatrix[2][0], 8.0))
return false;
if(!Compare(dissMatrix[2][1], 2.0))
return false;
// weighted Soergel
DiversityCalculator Soergel("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Soergel", 1000, true, false, false, false, false);
Soergel.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.55))
return false;
if(!Compare(dissMatrix[2][0], 0.615385))
return false;
if(!Compare(dissMatrix[2][1], 0.16981))
return false;
// weighted Bray-Curtis
DiversityCalculator BC("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Bray-Curtis", 1000, true, false, false, false, false);
BC.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.37931000))
return false;
if(!Compare(dissMatrix[2][0], 0.444440))
return false;
if(!Compare(dissMatrix[2][1], 0.092783500))
return false;
// weighted Fst
DiversityCalculator Fst("../unit-tests/SharedSeqs.env", "../unit-tests/SharedSeqs.tre", "Fst", 1000, true, false, false, false, false);
Fst.Dissimilarity("../unit-tests/temp", "UPGMA");
ReadDissMatrix("../unit-tests/temp.diss", dissMatrix);
if(!Compare(dissMatrix[1][0], 0.139560))
return false;
if(!Compare(dissMatrix[2][0], 0.18378390))
return false;
if(!Compare(dissMatrix[2][1], 0.043478190))
return false;
return true;
}
